MolNFT v1 · #91132 · protein
Crystal structure of wild type human CD38 in complex with naadp and adprp
4F46 · ADP-ribosyl cyclase 1: “Crystal structure of wild type human CD38 in complex with naadp and adprp”. X-ray diffraction, 2 ligands (DVN, DN4), 6 pockets (best druggability 0.75). MolNFT v1 #91132 on GenesisL1: 3D structure, binding…
- PDB
- 4F46
- Type
- protein
- Length
- 500 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ADP-ribosyl cyclase 1
- EC
- 3.2.2.5
- UniProt
- P28907
- Ligands
- DVN, DN4
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ADP-ribosyl cyclase 1 (EC 3.2.2.5) | protein | 248 | 44% helix, 15% strand | P28907 |
| B | ADP-ribosyl cyclase 1 (EC 3.2.2.5) | protein | 252 | 43% helix, 14% strand | P28907 |
Ligands and binding sites
- DVN · [[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5S)-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate · ligand · chains A
- DN4 · [[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(3-carboxypyridin-1-ium-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphate · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 714 | 0.75 | 0.80 | 85 | DN4 |
| 2 | 344 | 0.64 | 0.79 | 43 | DVN |
| 3 | 95 | 0.55 | 0.84 | 14 | empty |
| 4 | 86 | 0.53 | 0.84 | 16 | empty |
| 5 | 76 | 0.37 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 597 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 4F46 · Crystal structure of wild type human CD38 in complex with NAADP and ADPRP · the same entry in another collection · chain A against A, TM-score 1.00
- P28907 · AlphaFold monomer V2.0 prediction for ADP-ribosyl CYCLASE/CYCLIC ADP- ribose hydrolase 1… · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P28907
- Elsewhere: RCSB PDB 4F46 · PDBe 4F46 · UniProt P28907
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